* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/hsm.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘hsm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hsm’ version ‘0.2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘hsm’ can be installed ... [4s/11s] OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/12s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘hsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: hsm
> ### Title: Solves proximal operator of latent group lasso in Hierarchical
> ###   Sparse Modeling.
> ### Aliases: hsm
> 
> ### ** Examples
> 
> # The following example appears in Figure 7 of Yan & Bien (2015).
> # Generate map defining DAG.
> map <- matrix(0, ncol=2, nrow=8)
> map[1, ] <- c(1, 2)
> map[2, ] <- c(2, 7)
> map[3, ] <- c(3, 4)
> map[4, ] <- c(4, 6)
> map[5, ] <- c(6, 7)
> map[6, ] <- c(6, 8)
> map[7, ] <- c(3, 5)
> map[8, ] <- c(5, 6)
> # Assume one parameter per node.
> # Let parameter and node share the same index.
> var <- as.list(1:8)
> set.seed(100)
> y <- rnorm(8)
> result <- hsm(y=y, lam=0.5, map=map, var=var, get.penalval=TRUE)
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
hsm
 --- call from context --- 
path.find(u, map)
 --- call from argument --- 
!index %in% map[, 1] || is.na(map[which(map[, 1] == index), 2])
 --- R stacktrace ---
where 1: path.find(u, map)
where 2: paths(map = map, var = var, w = w)
where 3: hsm(y = y, lam = 0.5, map = map, var = var, get.penalval = TRUE)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (index, map) 
{
    if (!index %in% map[, 1] || is.na(map[which(map[, 1] == index), 
        2])) {
        return(list(index))
    }
    else {
        path <- list()
        ind <- 1
        right.index <- which(index == map[, 1])
        for (m in 1:length(right.index)) {
            path.right <- path.find(map[right.index[m], 2], map)
            for (n in 1:length(path.right)) {
                path[[ind]] <- c(index, path.right[[n]])
                ind <- ind + 1
            }
        }
        return(path)
    }
}
<bytecode: 0x2bef990>
<environment: namespace:hsm>
 --- function search by body ---
Function path.find in namespace hsm has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘hsm-vignette.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
hsm
 --- call from context --- 
path.find(u, map)
 --- call from argument --- 
!index %in% map[, 1] || is.na(map[which(map[, 1] == index), 2])
 --- R stacktrace ---
where 1: path.find(u, map)
where 2: paths(map, var)
where 3: eval(expr, envir, enclos)
where 4: eval(expr, envir, enclos)
where 5: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 6: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 7: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 8: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)))
where 10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, 
    debug = debug, last = i == length(out), use_try = stop_on_error != 
        2L, keep_warning = keep_warning, keep_message = keep_message, 
    output_handler = output_handler, include_timing = include_timing)
where 11: evaluate::evaluate(...)
where 12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), 
    keep_message = !isFALSE(options$message), stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options))
where 13: in_dir(input_dir(), expr)
where 14: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), 
    stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options)))
where 15: eng_r(options)
where 16: block_exec(params)
where 17: call_block(x)
where 18: process_group.block(group)
where 19: process_group(group)
where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 21: process_file(text, output)
where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 24: vweave_rmarkdown(...)
where 25: engine$weave(file, quiet = quiet, encoding = enc)
where 26: doTryCatch(return(expr), name, parentenv, handler)
where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 28: tryCatchList(expr, classes, parentenv, handlers)
where 29: tryCatch({
    engine$weave(file, quiet = quiet, encoding = enc)
    setwd(startdir)
    output <- find_vignette_product(name, by = "weave", engine = engine)
    if (!have.makefile && vignette_is_tex(output)) {
        texi2pdf(file = output, clean = FALSE, quiet = quiet)
        output <- find_vignette_product(name, by = "texi2pdf", 
            engine = engine)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 30: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/hsm.Rcheck/vign_test/hsm")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (index, map) 
{
    if (!index %in% map[, 1] || is.na(map[which(map[, 1] == index), 
        2])) {
        return(list(index))
    }
    else {
        path <- list()
        ind <- 1
        right.index <- which(index == map[, 1])
        for (m in 1:length(right.index)) {
            path.right <- path.find(map[right.index[m], 2], map)
            for (n in 1:length(path.right)) {
                path[[ind]] <- c(index, path.right[[n]])
                ind <- ind + 1
            }
        }
        return(path)
    }
}
<bytecode: 0x4b7d510>
<environment: namespace:hsm>
 --- function search by body ---
Function path.find in namespace hsm has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical

* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/hsm.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:38.11, 31.23 + 6.64